New finite element iterative methods for solving a nonuniform ionic size modified Poisson-Boltzmann equation

MaRDI QIDQ4602018zbMATH OpenFDO

Authors Dexuan Xie

Publication date 25 January 2018

Full work available at URL http://www.math.ualberta.ca/ijnam/Volume-14-2017/No-4-17/2017-45-12.pdf

zbMATH Keywords

electrostaticsfinite element methodionic size effectsnonlinear successive overrelaxationPoisson-Boltzmann equation

Mathematics Subject Classification ID

Finite element, Rayleigh-Ritz and Galerkin methods for boundary value problems involving PDEs (65N30) Computational methods for problems pertaining to biology (92-08) Biochemistry, molecular biology (92C40)

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Cited in

(18)

• On the analysis and application of an ion size-modified Poisson-Boltzmann equation
• A Newton-like iterative method implemented in the DelPhi for solving the nonlinear Poisson-Boltzmann equation
• An efficient finite element iterative method for solving a nonuniform size modified Poisson-Boltzmann ion channel model
• A finite element iterative solver for a PNP ion channel model with Neumann boundary condition and membrane surface charge
• Linear-scaling selected inversion based on hierarchical interpolative factorization for self Green's function for modified Poisson-Boltzmann equation in two dimensions
• A hybrid solver of size modified Poisson-Boltzmann equation by domain decomposition, finite element, and finite difference
• A simple and efficient technique to accelerate the computation of a nonlocal dielectric model for electrostatics of biomolecule
• The solution of the Poisson-Boltzmann equation between two spheres: Modified iterative method
• A new box iterative method for a class of nonlinear interface problems with application in solving Poisson-Boltzmann equation
• An effective minimization protocol for solving a size-modified Poisson-Boltzmann equation for biomolecule in ionic solvent
• Solving fluctuation-enhanced Poisson-Boltzmann equations
• Fast iterative method for local steric Poisson-Boltzmann theories in biomolecular solvation
• Finite element approximation to a finite-size modified Poisson-Boltzmann equation
• An efficient finite element solver for a nonuniform size-modified Poisson-Nernst-Planck ion channel model
• An efficient finite element solver for a nonlocal size modified Poisson-Boltzmann model of proteins in multi-species ionic solutions
• A nonlocal modified Poisson-Boltzmann equation and finite element solver for computing electrostatics of biomolecules
• Shallow neural networks for solving nonuniform size-modified Poisson-Boltzmann equations
• Nonlocal nonuniform size modified Poisson-Boltzmann model and efficient finite element solver for protein electrostatics and ion distributions

Describes a project that uses

Uses Software

• AFMPB
• AQUASOL
• SDPBS
• MIBPB
• Python

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